Capn2 (calpain 2) - Rat Genome Database

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Gene: Capn2 (calpain 2) Rattus norvegicus
Analyze
Symbol: Capn2
Name: calpain 2
RGD ID: 2268
Description: Enables calcium ion binding activity; cytoskeletal protein binding activity; and enzyme binding activity. Contributes to calcium-dependent cysteine-type endopeptidase activity. Involved in several processes, including cellular response to interferon-beta; positive regulation of cell death; and positive regulation of myoblast fusion. Located in several cellular components, including external side of plasma membrane; focal adhesion; and neuronal cell body. Colocalizes with mitochondrial intermembrane space. Biomarker of hypertrophic cardiomyopathy and sciatic neuropathy. Orthologous to human CAPN2 (calpain 2); PARTICIPATES IN the proteolytic pathway involving calcium-dependent proteases; Alzheimer's disease pathway; apoptotic cell death pathway; INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: calcium-activated neutral proteinase 2; calpain 2, (m/II) large subunit; calpain II; calpain M-type; calpain-2 catalytic subunit; calpain-2 large subunit; CANP 2; M-calpain; millimolar-calpain
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21394,150,244 - 94,200,969 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1394,150,240 - 94,200,969 (-)Ensembl
Rnor_6.013100,878,649 - 100,928,811 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13100,878,650 - 100,928,811 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013105,814,749 - 105,864,911 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41398,473,367 - 98,524,463 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11398,662,303 - 98,713,399 (-)NCBI
Celera1393,683,410 - 93,734,060 (-)NCBICelera
Cytogenetic Map13q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2,6-dinitrotoluene  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-[1-hydroxy-2-[4-(phenylmethyl)-1-piperidinyl]propyl]phenol  (EXP)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-aminophenol  (EXP)
4-hydroxynon-2-enal  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6alpha-methylprednisolone  (EXP)
8-Br-cAMP  (ISO)
9-cis-retinoic acid  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
BAPTA  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bucladesine  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
calcitriol  (ISO)
Calpeptin  (EXP)
cantharidin  (ISO)
carbamazepine  (ISO)
carbon disulfide  (EXP)
carbon nanotube  (ISO)
casticin  (ISO)
chlordecone  (ISO)
chloroacetic acid  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
dantrolene  (EXP)
DDT  (EXP)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (ISO)
dibenzo[a,l]pyrene  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
endosulfan  (EXP)
ethanol  (EXP,ISO)
fipronil  (EXP)
fisetin  (ISO)
folic acid  (ISO)
fumonisin B1  (ISO)
geneticin  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (EXP,ISO)
hydroquinone  (ISO)
indometacin  (EXP,ISO)
isoflurane  (EXP)
isoprenaline  (EXP)
ivermectin  (ISO)
lipopolysaccharide  (ISO)
medroxyprogesterone acetate  (ISO)
menadione  (ISO)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
microcystin-LR  (ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodimethylamine  (ISO)
nickel atom  (ISO)
nimesulide  (EXP)
nitroglycerin  (EXP)
NS-398  (EXP)
paracetamol  (ISO)
paraquat  (EXP)
phenethyl isothiocyanate  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
propiconazole  (ISO)
quercetin  (EXP,ISO)
raloxifene  (ISO)
SB 431542  (ISO)
sodium arsenite  (EXP,ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP,ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (EXP)
Triptolide  (ISO)
tungsten  (ISO)
ursodeoxycholic acid  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
vorinostat  (ISO)
Z-Val-Phe-H  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Alexa A, etal., J Biol Chem. 2004 May 7;279(19):20118-26. Epub 2004 Feb 19.
2. Balcerzak D, etal., J Cell Sci. 1995 May;108 ( Pt 5):2077-82.
3. Bevers MB, etal., J Neurochem. 2009 Mar;108(5):1237-50. doi: 10.1111/j.1471-4159.2008.05860.x. Epub 2009 Jan 22.
4. Brulé C, etal., Biochimie. 2010 Dec;92(12):1923-33. doi: 10.1016/j.biochi.2010.09.003. Epub 2010 Sep 17.
5. Chang H, etal., J Cell Biochem. 2011 Feb;112(2):571-80. doi: 10.1002/jcb.22947.
6. DeLuca CI, etal., Biochim Biophys Acta 1993 Oct 19;1216(1):81-93.
7. Dourdin N, etal., Exp Cell Res. 1997 Sep 15;235(2):385-94. doi: 10.1006/excr.1997.3684.
8. Enns DL, etal., Eur J Appl Physiol. 2007 Jul;100(4):445-55. Epub 2007 Apr 12.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. Graham-Siegenthaler K, etal., J Biol Chem 1994 Dec 2;269(48):30457-60.
11. Hanna RA, etal., FEBS Lett. 2007 Jun 26;581(16):2894-8. Epub 2007 May 25.
12. Hanna RA, etal., Nature. 2008 Nov 20;456(7220):409-12. doi: 10.1038/nature07451.
13. Hosfield CM, etal., EMBO J. 1999 Dec 15;18(24):6880-9.
14. Hosfield CM, etal., J Mol Biol. 2004 Oct 29;343(4):1049-53.
15. Kaneko Y, etal., Histochem Cell Biol. 2014 Apr;141(4):423-30. doi: 10.1007/s00418-013-1165-y. Epub 2013 Nov 23.
16. Latronico T, etal., PLoS One. 2013;8(2):e49656. doi: 10.1371/journal.pone.0049656. Epub 2013 Feb 4.
17. Li HL, etal., Cell Signal. 1998 Feb;10(2):137-42.
18. Luke CJ, etal., Cell. 2007 Sep 21;130(6):1108-19.
19. Matsumoto A, etal., Acta Histochem. 2014 Jun;116(5):936-42. doi: 10.1016/j.acthis.2014.03.006. Epub 2014 Apr 16.
20. MGD data from the GO Consortium
21. Moldoveanu T, etal., Nature. 2008 Nov 20;456(7220):404-8.
22. NCBI rat LocusLink and RefSeq merged data July 26, 2002
23. Ozaki T, etal., Biochim Biophys Acta. 2009 Dec;1793(12):1848-59. doi: 10.1016/j.bbamcr.2009.10.002. Epub 2009 Oct 13.
24. Pipeline to import KEGG annotations from KEGG into RGD
25. Ray SK, etal., J Neurosci Res. 2002 Nov 15;70(4):561-9. doi: 10.1002/jnr.10414.
26. RGD automated data pipeline
27. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. RGD automated import pipeline for gene-chemical interactions
29. Sheng JJ, etal., J Cell Physiol. 2015 Nov;230(11):2743-54. doi: 10.1002/jcp.24999.
30. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
31. Tamada Y, etal., Brain Res. 2005 Jul 19;1050(1-2):148-55.
32. Tsuji T, etal., Neurosci Lett. 1998 May 29;248(2):109-12.
33. Vermaelen M, etal., Am J Physiol Cell Physiol. 2007 May;292(5):C1723-31. Epub 2006 Dec 20.
34. Wang CF and Huang YS, Mol Cell Biol. 2012 Aug;32(16):3321-32. doi: 10.1128/MCB.00296-12. Epub 2012 Jun 18.
35. Xu W, etal., J Zhejiang Univ Sci. 2004 Jun;5(6):743-8.
36. Zang Y, etal., Brain Behav Immun. 2015 Feb;44:37-47. doi: 10.1016/j.bbi.2014.08.003. Epub 2014 Aug 20.
37. Zhang S, etal., Medicine (Baltimore). 2015 Jan;94(4):e445. doi: 10.1097/MD.0000000000000445.
38. Zhang Z, etal., J Neurotrauma. 2007 Mar;24(3):460-72.
39. Zhao X, etal., J Cereb Blood Flow Metab. 1998 Feb;18(2):161-7. doi: 10.1097/00004647-199802000-00006.
Additional References at PubMed
PMID:7635186   PMID:10949052   PMID:11102442   PMID:11342050   PMID:12150984   PMID:12534936   PMID:14559243   PMID:14618389   PMID:15132950   PMID:15489334   PMID:16433929   PMID:17712625  
PMID:18258589   PMID:18415939   PMID:19056867   PMID:19199708   PMID:19318376   PMID:19861418   PMID:20211186   PMID:20298691   PMID:20945043   PMID:21145877   PMID:21423176   PMID:21549862  
PMID:21849499   PMID:22547201   PMID:22555453   PMID:22870316   PMID:23376485   PMID:23495712   PMID:25270371   PMID:25820554   PMID:26086870   PMID:27622212   PMID:28342779   PMID:28559121  
PMID:29413901   PMID:29476059   PMID:29477696   PMID:29772491   PMID:30423475   PMID:33456665   PMID:33517223  


Genomics

Comparative Map Data
Capn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21394,150,244 - 94,200,969 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1394,150,240 - 94,200,969 (-)Ensembl
Rnor_6.013100,878,649 - 100,928,811 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13100,878,650 - 100,928,811 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013105,814,749 - 105,864,911 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41398,473,367 - 98,524,463 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11398,662,303 - 98,713,399 (-)NCBI
Celera1393,683,410 - 93,734,060 (-)NCBICelera
Cytogenetic Map13q26NCBI
CAPN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1223,701,593 - 223,776,018 (+)EnsemblGRCh38hg38GRCh38
GRCh381223,701,597 - 223,776,018 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371223,889,299 - 223,963,720 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361221,966,742 - 222,030,343 (+)NCBINCBI36hg18NCBI36
Build 341220,206,935 - 220,270,453NCBI
Celera1197,044,917 - 197,119,643 (+)NCBI
Cytogenetic Map1q41NCBI
HuRef1194,501,759 - 194,576,134 (+)NCBIHuRef
CHM1_11225,161,051 - 225,236,057 (+)NCBICHM1_1
Capn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391182,294,818 - 182,345,175 (-)NCBIGRCm39mm39
GRCm39 Ensembl1182,294,825 - 182,345,173 (-)Ensembl
GRCm381182,467,253 - 182,517,610 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1182,467,260 - 182,517,608 (-)EnsemblGRCm38mm10GRCm38
MGSCv371184,397,390 - 184,447,614 (-)NCBIGRCm37mm9NCBIm37
MGSCv361184,303,935 - 184,354,199 (-)NCBImm8
Celera1189,509,702 - 189,560,154 (-)NCBICelera
Cytogenetic Map1H5NCBI
Capn2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555201,286,356 - 1,315,328 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555201,287,829 - 1,315,318 (-)NCBIChiLan1.0ChiLan1.0
CAPN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11204,346,476 - 204,410,137 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1204,335,573 - 204,409,150 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01199,335,582 - 199,399,267 (+)NCBIMhudiblu_PPA_v0panPan3
CAPN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1740,333,379 - 40,367,158 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl740,334,012 - 40,377,037 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha739,815,620 - 39,853,714 (-)NCBI
ROS_Cfam_1.0740,166,074 - 40,204,194 (-)NCBI
UMICH_Zoey_3.1740,007,852 - 40,045,930 (-)NCBI
UNSW_CanFamBas_1.0740,016,382 - 40,054,477 (-)NCBI
UU_Cfam_GSD_1.0740,285,433 - 40,323,542 (-)NCBI
Capn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934453,814,785 - 53,867,532 (-)NCBI
SpeTri2.0NW_004936526879,765 - 932,682 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAPN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1019,758,762 - 19,851,989 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11019,758,824 - 19,820,241 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CAPN2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1255,845,873 - 5,905,464 (-)NCBI
ChlSab1.1 Ensembl255,846,298 - 5,905,402 (-)Ensembl
Vero_WHO_p1.0NW_0236660556,059,645 - 6,119,546 (-)NCBI

Position Markers
D13Wox20  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map13q26UniSTS
RH136960  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21394,150,268 - 94,150,456 (+)MAPPERmRatBN7.2
Rnor_6.013100,878,674 - 100,878,861NCBIRnor6.0
Rnor_5.013105,814,774 - 105,814,961UniSTSRnor5.0
RGSC_v3.41398,473,392 - 98,473,579UniSTSRGSC3.4
Celera1393,683,435 - 93,683,622UniSTS
Cytogenetic Map13q26UniSTS
RH138755  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21394,192,571 - 94,192,736 (+)MAPPERmRatBN7.2
Rnor_6.013100,920,414 - 100,920,578NCBIRnor6.0
Rnor_5.013105,856,514 - 105,856,678UniSTSRnor5.0
RGSC_v3.41398,516,066 - 98,516,230UniSTSRGSC3.4
Celera1393,725,663 - 93,725,827UniSTS
RH 3.4 Map13632.9UniSTS
Cytogenetic Map13q26UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:366
Count of miRNA genes:212
Interacting mature miRNAs:237
Transcripts:ENSRNOT00000045326
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 56 40 19 40 8 11 74 35 39 11 8
Low 1 1 1 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000045326   ⟹   ENSRNOP00000046509
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1394,150,245 - 94,200,969 (-)Ensembl
Rnor_6.0 Ensembl13100,878,650 - 100,928,811 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097310   ⟹   ENSRNOP00000086926
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1394,150,240 - 94,200,561 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118482   ⟹   ENSRNOP00000076404
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1394,153,195 - 94,200,969 (-)Ensembl
RefSeq Acc Id: NM_017116   ⟹   NP_058812
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21394,150,244 - 94,200,969 (-)NCBI
Rnor_6.013100,878,649 - 100,928,811 (-)NCBI
Rnor_5.013105,814,749 - 105,864,911 (-)NCBI
RGSC_v3.41398,473,367 - 98,524,463 (-)RGD
Celera1393,683,410 - 93,734,060 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058812   ⟸   NM_017116
- UniProtKB: Q07009 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000046509   ⟸   ENSRNOT00000045326
RefSeq Acc Id: ENSRNOP00000076404   ⟸   ENSRNOT00000118482
RefSeq Acc Id: ENSRNOP00000086926   ⟸   ENSRNOT00000097310
Protein Domains
Calpain catalytic   EF-hand

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699078
Promoter ID:EPDNEW_R9603
Type:initiation region
Name:Capn2_1
Description:calpain 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013100,928,488 - 100,928,548EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2268 AgrOrtholog
Ensembl Genes ENSRNOG00000034015 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000046509 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000045326 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5621252 IMAGE-MGC_LOAD
InterPro C2_III UniProtKB/Swiss-Prot
  Calpain_cysteine_protease UniProtKB/Swiss-Prot
  Calpain_domain_III UniProtKB/Swiss-Prot
  Calpain_III UniProtKB/Swiss-Prot
  Calpain_III_sf UniProtKB/Swiss-Prot
  CAPN2 UniProtKB/Swiss-Prot
  EF-hand-dom_pair UniProtKB/Swiss-Prot
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot
  EF_hand_dom UniProtKB/Swiss-Prot
  EFh_PEF_CAPN2 UniProtKB/Swiss-Prot
  Papain-like_cys_pep_sf UniProtKB/Swiss-Prot
  Pept_cys_AS UniProtKB/Swiss-Prot
  Peptidase_C2_calpain_cat UniProtKB/Swiss-Prot
KEGG Report rno:29154 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72508 IMAGE-MGC_LOAD
NCBI Gene 29154 ENTREZGENE
PANTHER PTHR10183:SF268 UniProtKB/Swiss-Prot
Pfam Calpain_III UniProtKB/Swiss-Prot
  EF-hand_8 UniProtKB/Swiss-Prot
  Peptidase_C2 UniProtKB/Swiss-Prot
PhenoGen Capn2 PhenoGen
PRINTS CALPAIN UniProtKB/Swiss-Prot
PROSITE CALPAIN_CAT UniProtKB/Swiss-Prot
  EF_HAND_1 UniProtKB/Swiss-Prot
  EF_HAND_2 UniProtKB/Swiss-Prot
  THIOL_PROTEASE_CYS UniProtKB/Swiss-Prot
SMART calpain_III UniProtKB/Swiss-Prot
  CysPc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot
  SSF49758 UniProtKB/Swiss-Prot
  SSF54001 UniProtKB/Swiss-Prot
UniProt CAN2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-27 Capn2  calpain 2  Capn2  calpain 2, (m/II) large subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-06 Capn2  calpain 2, (m/II) large subunit  Capn2  calpain 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Capn2  calpain 2      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_protein 700 amino acid protein 69794
gene_transcript contains 21 exons 69794